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Merge pull request #21606 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
Nicola Soranzo
2026-01-17 11:21:51 +00:00
committed by GitHub
parent c559d7f1bc 223b71cac4
commit a467c8d885
5 changed files with 50 additions and 44 deletions
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lib/galaxy/dependencies/dev-requirements.txt
+14 -11
View File
@@ -46,7 +46,8 @@ darker==3.0.0
darkgraylib==2.4.1
decorator==5.2.1
defusedxml==0.7.1
docutils==0.21.2
docutils==0.21.2 ; python_full_version < '3.11'
docutils==0.22.4 ; python_full_version >= '3.11'
dogpile-cache==1.4.1 ; python_full_version < '3.10'
dogpile-cache==1.5.0 ; python_full_version >= '3.10'
enum-tools==0.12.0 ; python_full_version >= '3.10'
@@ -77,7 +78,7 @@ isodate==0.7.2 ; python_full_version < '3.11'
isort==6.1.0 ; python_full_version < '3.10'
isort==7.0.0 ; python_full_version >= '3.10'
jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-context==6.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-context==6.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-functools==4.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
jinja2==3.1.6
@@ -91,9 +92,10 @@ junit-xml==1.9
keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
kiwisolver==1.4.7 ; python_full_version < '3.10'
kiwisolver==1.4.9 ; python_full_version >= '3.10'
librt==0.7.7 ; platform_python_implementation != 'PyPy'
librt==0.7.8 ; platform_python_implementation != 'PyPy'
lxml==6.0.2
markdown-it-py==3.0.0
markdown-it-py==3.0.0 ; python_full_version < '3.11'
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
markdown-it-reporter==0.0.2
markupsafe==3.0.3
matplotlib==3.9.4 ; python_full_version < '3.10'
@@ -110,11 +112,12 @@ multidict==6.7.0
mypy==1.19.1
mypy-extensions==1.1.0
myst-parser==3.0.1 ; python_full_version < '3.10'
myst-parser==4.0.1 ; python_full_version >= '3.10'
myst-parser==4.0.1 ; python_full_version == '3.10.*'
myst-parser==5.0.0 ; python_full_version >= '3.11'
nh3==0.3.2
numpy==2.0.2 ; python_full_version < '3.10'
numpy==2.2.6 ; python_full_version == '3.10.*'
numpy==2.4.0 ; python_full_version >= '3.11'
numpy==2.4.1 ; python_full_version >= '3.11'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
owlrl==6.0.2 ; python_full_version < '3.10'
@@ -186,7 +189,6 @@ roc-validator==0.4.2 ; python_full_version < '3.9.20'
roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
roc-validator==0.8.0 ; python_full_version >= '3.10'
roman-numerals==4.1.0 ; python_full_version >= '3.11'
roman-numerals-py==4.1.0 ; python_full_version >= '3.11'
rpds-py==0.27.1 ; python_full_version < '3.10'
rpds-py==0.30.0 ; python_full_version >= '3.10'
ruamel-yaml==0.18.17
@@ -197,7 +199,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10'
schema-salad==8.9.20251102115403
scipy==1.13.1 ; python_full_version < '3.10'
scipy==1.15.3 ; python_full_version == '3.10.*'
scipy==1.16.3 ; python_full_version >= '3.11'
scipy==1.17.0 ; python_full_version >= '3.11'
secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
secretstorage==3.5.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
selenium==4.32.0 ; python_full_version < '3.10'
@@ -209,8 +211,9 @@ snowballstemmer==3.0.1
sortedcontainers==2.4.0
sphinx==7.4.7 ; python_full_version < '3.10'
sphinx==8.1.3 ; python_full_version == '3.10.*'
sphinx==8.2.3 ; python_full_version >= '3.11'
sphinx-rtd-theme==3.0.2
sphinx==9.0.4 ; python_full_version == '3.11.*'
sphinx==9.1.0 ; python_full_version >= '3.12'
sphinx-rtd-theme==3.1.0
sphinxcontrib-applehelp==2.0.0
sphinxcontrib-devhelp==2.0.0
sphinxcontrib-htmlhelp==2.1.0
@@ -227,7 +230,7 @@ testfixtures==10.0.0 ; python_full_version >= '3.11'
text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.3.0 ; python_full_version <= '3.11'
tomli==2.4.0 ; python_full_version <= '3.11'
total-perspective-vortex==3.1.3
trio==0.31.0 ; python_full_version < '3.10'
trio==0.32.0 ; python_full_version >= '3.10'
lib/galaxy/dependencies/pinned-lint-requirements.txt
+1 -1
View File
@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
mccabe==0.7.0
pycodestyle==2.14.0
pyflakes==3.4.0
ruff==0.14.11
ruff==0.14.13
lib/galaxy/dependencies/pinned-requirements.txt
+24 -22
View File
@@ -11,11 +11,11 @@ aiohttp==3.13.3
aioitertools==0.13.0
aiosignal==1.4.0
alembic==1.16.5 ; python_full_version < '3.10'
alembic==1.18.0 ; python_full_version >= '3.10'
alembic==1.18.1 ; python_full_version >= '3.10'
amqp==5.3.1
annotated-doc==0.0.4
annotated-types==0.7.0
anthropic==0.75.0
anthropic==0.76.0
anyio==4.12.1
apispec==6.8.4 ; python_full_version < '3.10'
apispec==6.9.0 ; python_full_version >= '3.10'
@@ -72,7 +72,7 @@ cwl-upgrader==1.2.14 ; python_full_version >= '3.10'
cwl-utils==0.40
cwltool==3.1.20251031082601 ; python_full_version < '3.10'
cwltool==3.1.20260108082145 ; python_full_version >= '3.10'
cyclopts==4.4.4 ; python_full_version >= '3.10'
cyclopts==4.5.0 ; python_full_version >= '3.10'
defusedxml==0.7.1
deprecated==1.3.1
deprecation==2.1.0
@@ -83,7 +83,8 @@ dnspython==2.7.0 ; python_full_version < '3.10'
dnspython==2.8.0 ; python_full_version >= '3.10'
docopt==0.6.2
docstring-parser==0.17.0
docutils==0.21.2
docutils==0.21.2 ; python_full_version < '3.11'
docutils==0.22.4 ; python_full_version >= '3.11'
dparse==0.6.4
edam-ontology==1.25.3
email-validator==2.3.0
@@ -94,7 +95,7 @@ executing==2.2.1 ; python_full_version >= '3.10'
fakeredis==2.33.0 ; python_full_version >= '3.10'
fastapi==0.128.0
fastavro==1.12.1 ; sys_platform != 'emscripten'
fastmcp==2.14.2 ; python_full_version >= '3.10'
fastmcp==2.14.3 ; python_full_version >= '3.10'
filelock==3.19.1 ; python_full_version < '3.10'
filelock==3.20.3 ; python_full_version >= '3.10'
fissix==24.4.24
@@ -103,14 +104,14 @@ fs==2.4.16
fsspec==2025.10.0 ; python_full_version < '3.10'
fsspec==2026.1.0 ; python_full_version >= '3.10'
future==1.0.0
genai-prices==0.0.50
genai-prices==0.0.51
google-api-core==2.29.0
google-auth==2.47.0
google-cloud-batch==0.20.0
google-genai==1.47.0 ; python_full_version < '3.10'
google-genai==1.57.0 ; python_full_version >= '3.10'
google-genai==1.59.0 ; python_full_version >= '3.10'
googleapis-common-protos==1.72.0
gravity @ git+https://github.com/nsoranzo/gravity.git@a60c911e61c784d37d3eb334c1c68288d2c06ef3
gravity @ git+https://github.com/nsoranzo/gravity.git@7c5f457424658ee904694f5566e61b562bce7ed6
greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64')
greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64')
griffe==1.14.0 ; python_full_version < '3.10'
@@ -140,7 +141,7 @@ isa-rwval==0.10.11
isal==1.8.0
isodate==0.7.2 ; python_full_version < '3.11'
jaraco-classes==3.4.0 ; python_full_version >= '3.10'
jaraco-context==6.0.2 ; python_full_version >= '3.10'
jaraco-context==6.1.0 ; python_full_version >= '3.10'
jaraco-functools==4.4.0 ; python_full_version >= '3.10'
jeepney==0.9.0 ; python_full_version >= '3.10' and sys_platform == 'linux'
jinja2==3.1.6
@@ -157,14 +158,15 @@ lagom==2.7.7
legacy-cgi==2.6.4 ; python_full_version >= '3.13'
limits==4.2 ; python_full_version < '3.10'
limits==5.6.0 ; python_full_version >= '3.10'
logfire==4.17.0 ; python_full_version >= '3.10'
logfire-api==4.17.0
logfire==4.19.0 ; python_full_version >= '3.10'
logfire-api==4.19.0
lupa==2.6 ; python_full_version >= '3.10'
lxml==6.0.2
mako==1.3.10
markdown==3.9 ; python_full_version < '3.10'
markdown==3.10 ; python_full_version >= '3.10'
markdown-it-py==3.0.0
markdown-it-py==3.0.0 ; python_full_version < '3.11'
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
markupsafe==3.0.3
mcp==1.25.0 ; python_full_version >= '3.10'
mdurl==0.1.2
@@ -186,7 +188,7 @@ nodejs-wheel==22.20.0
nodejs-wheel-binaries==22.20.0
numpy==2.0.2 ; python_full_version < '3.10'
numpy==2.2.6 ; python_full_version == '3.10.*'
numpy==2.4.0 ; python_full_version >= '3.11'
numpy==2.4.1 ; python_full_version >= '3.11'
oauthlib==3.3.1
openai==2.15.0
openapi-pydantic==0.5.1 ; python_full_version >= '3.10'
@@ -215,12 +217,12 @@ pebble==5.1.3
pillow==11.3.0 ; python_full_version < '3.10'
pillow==12.1.0 ; python_full_version >= '3.10'
platformdirs==4.5.1 ; python_full_version >= '3.10'
prometheus-client==0.23.1 ; python_full_version >= '3.10'
prometheus-client==0.24.1 ; python_full_version >= '3.10'
prompt-toolkit==3.0.52
propcache==0.4.1
proto-plus==1.27.0
protobuf==5.29.5 ; python_full_version < '3.10'
protobuf==6.33.3 ; python_full_version >= '3.10'
protobuf==6.33.4 ; python_full_version >= '3.10'
prov==1.5.1
psutil==7.2.1
pulsar-galaxy-lib==0.15.13
@@ -232,14 +234,14 @@ pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementat
pycryptodome==3.23.0
pydantic==2.12.5
pydantic-ai==0.8.1 ; python_full_version < '3.10'
pydantic-ai==1.41.0 ; python_full_version >= '3.10'
pydantic-ai==1.44.0 ; python_full_version >= '3.10'
pydantic-ai-slim==0.8.1 ; python_full_version < '3.10'
pydantic-ai-slim==1.41.0 ; python_full_version >= '3.10'
pydantic-ai-slim==1.44.0 ; python_full_version >= '3.10'
pydantic-core==2.41.5
pydantic-evals==0.8.1 ; python_full_version < '3.10'
pydantic-evals==1.41.0 ; python_full_version >= '3.10'
pydantic-evals==1.44.0 ; python_full_version >= '3.10'
pydantic-graph==0.8.1 ; python_full_version < '3.10'
pydantic-graph==1.41.0 ; python_full_version >= '3.10'
pydantic-graph==1.44.0 ; python_full_version >= '3.10'
pydantic-settings==2.11.0 ; python_full_version < '3.10'
pydantic-settings==2.12.0 ; python_full_version >= '3.10'
pydantic-tes==0.2.0
@@ -275,7 +277,7 @@ rdflib==7.5.0 ; python_full_version >= '3.10'
redis==7.1.0 ; python_full_version >= '3.10'
referencing==0.36.2
refgenconf==0.12.2
regex==2025.11.3
regex==2026.1.15
repoze-lru==0.7
requests==2.32.5
requests-oauthlib==2.0.0
@@ -320,11 +322,11 @@ tenacity==9.1.2
text-unidecode==1.3
tifffile==2024.8.30 ; python_full_version < '3.10'
tifffile==2025.5.10 ; python_full_version == '3.10.*'
tifffile==2025.12.20 ; python_full_version >= '3.11'
tifffile==2026.1.14 ; python_full_version >= '3.11'
tiktoken==0.12.0 ; python_full_version >= '3.10'
tinydb==4.8.2
tokenizers==0.22.2 ; sys_platform != 'emscripten'
tomli==2.3.0 ; python_full_version < '3.11'
tomli==2.4.0 ; python_full_version < '3.11'
tornado==6.5.4
tqdm==4.67.1
tuspy==1.1.0
lib/galaxy/dependencies/pinned-test-requirements.txt
+6 -5
View File
@@ -69,9 +69,10 @@ jsonschema-specifications==2025.9.1
junit-xml==1.9
kiwisolver==1.4.7 ; python_full_version < '3.10'
kiwisolver==1.4.9 ; python_full_version >= '3.10'
librt==0.7.7 ; platform_python_implementation != 'PyPy'
librt==0.7.8 ; platform_python_implementation != 'PyPy'
lxml==6.0.2
markdown-it-py==3.0.0
markdown-it-py==3.0.0 ; python_full_version < '3.11'
markdown-it-py==4.0.0 ; python_full_version >= '3.11'
markupsafe==3.0.3
matplotlib==3.9.4 ; python_full_version < '3.10'
matplotlib==3.10.8 ; python_full_version >= '3.10'
@@ -85,7 +86,7 @@ mypy==1.19.1
mypy-extensions==1.1.0
numpy==2.0.2 ; python_full_version < '3.10'
numpy==2.2.6 ; python_full_version == '3.10.*'
numpy==2.4.0 ; python_full_version >= '3.11'
numpy==2.4.1 ; python_full_version >= '3.11'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
owlrl==6.0.2 ; python_full_version < '3.10'
@@ -157,7 +158,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10'
schema-salad==8.9.20251102115403
scipy==1.13.1 ; python_full_version < '3.10'
scipy==1.15.3 ; python_full_version == '3.10.*'
scipy==1.16.3 ; python_full_version >= '3.11'
scipy==1.17.0 ; python_full_version >= '3.11'
selenium==4.32.0 ; python_full_version < '3.10'
selenium==4.39.0 ; python_full_version >= '3.10'
seletools==1.5.0
@@ -173,7 +174,7 @@ testfixtures==10.0.0 ; python_full_version >= '3.11'
text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.3.0 ; python_full_version <= '3.11'
tomli==2.4.0 ; python_full_version <= '3.11'
total-perspective-vortex==3.1.3
trio==0.31.0 ; python_full_version < '3.10'
trio==0.32.0 ; python_full_version >= '3.10'
lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+5 -5
View File
@@ -1,11 +1,11 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
annotated-types==0.7.0
boto3-stubs==1.42.25
botocore-stubs==1.42.25
boto3-stubs==1.42.30
botocore-stubs==1.42.30
cffi==2.0.0 ; platform_python_implementation != 'PyPy'
cryptography==46.0.3
librt==0.7.7 ; platform_python_implementation != 'PyPy'
librt==0.7.8 ; platform_python_implementation != 'PyPy'
lxml-stubs==0.5.1
mypy==1.19.1
mypy-boto3-s3==1.42.21
@@ -14,8 +14,8 @@ pathspec==1.0.3
pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
pydantic==2.12.5
pydantic-core==2.41.5
tomli==2.3.0 ; python_full_version < '3.11'
types-awscrt==0.30.0
tomli==2.4.0 ; python_full_version < '3.11'
types-awscrt==0.31.1
types-bleach==6.3.0.20251115
types-boto==2.49.18.20241019
types-contextvars==2.4.7.3